/*    Copyright 2010 Tobias Marschall
 *
 *    This file is part of MoSDi.
 *
 *    MoSDi is free software: you can redistribute it and/or modify
 *    it under the terms of the GNU General Public License as published by
 *    the Free Software Foundation, either version 3 of the License, or
 *    (at your option) any later version.
 *
 *    MoSDi is distributed in the hope that it will be useful,
 *    but WITHOUT ANY WARRANTY; without even the implied warranty of
 *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *    GNU General Public License for more details.
 *
 *    You should have received a copy of the GNU General Public License
 *    along with MoSDi.  If not, see <http://www.gnu.org/licenses/>.
 */

package mosdi.tests;

import junit.framework.TestCase;
import mosdi.fa.Alphabet;
import mosdi.fa.FiniteMemoryTextModel;
import mosdi.fa.MarkovianTextModel;

public class ReverseTextModelTest extends TestCase {
	
	//private final String background = "ATCTAACGTTCGTTCATGGAGCTGGGATGGCGCTTAATACGGGTGTAAGCGATGTAGAATATGAGGCTGCCTTCGCAAGTGGGAACACGAACCTCGAAAC";
	private final String background = "GGTAGGCTCGTGCAAAGGCGGGTTCTTCTCTTCGCAAGATTTAATAGTACTGTTTTACGCTTGTACGACCATAATGAATGTTCAATCTCTATAAGCATTTCAGTGTTAAGTACTGCGTGATCAATGCTGGTTTCCGGGCCTAAATAGGCGCCGACATCCATTCTCTTTGGCCTCGGAGCAATGACCTGGTATCAGATTCAACTAGGAGTCCTCGGTTTATATACTCGATACCGTGTTCCGTTAAATGGGACCGTGTAAGGAAGTCGAATCGTAGATACTAGCATCGGGACCACTTACGGCAGGACAAGCCATTCCCGGGCGCTATGTCAGTCCGTCGTATAACTATTATACCTTCACACCTCTCCGACCGGCTGCATACCGCGTAGTCCCACATAAGAACGTATCCTTGCATTTGGTATTCGCTCCTCTATGGGTTACTAATTAACGATTTCTGATACTTGATATTTCCTATAACCTAAGCAGGCCATAAACAATGCGAGAGCATACCGGCGGCAATCCTTTTCACTACTGGTATTCGACGTTACTGACAATGAAGGTAGAGTCGGACCGTTACGTTAAAGTGAACGCGCAGGACAAGAGGTACGTGGTGCGCGATAAGGAGGCCCCGAGCGACTGGAGGGTTGCTTAGGATAACGGACGGGGAAAATGGAAGCGCGTATATTGACACTCTTGACCTGACGCGACAGCCCCTTAACGACCCTACTTGGTTATTTCCTTCATGAATTTTGTGCAGCAAGTGGGTGAGCGCCACATTCTTCCGAAGCCGGTTCCCGAGATTGAACCCCGACTTGGCTATATACCGCATGTCATAGCTACGGATGACTACCAGGAATGGCCAAACGCTCAGGCTCTGCTGATGCATCTAAATACCAGTAGCGCCGATCCAACCCTCGATTACTGGTTTTCTTTTCGAGTAGAAACTTAAGAGCCACAACTGGTACACCGGCGCTCTATAGCCATAGCTCACCGTTCACATAGCGACGGCTGGCACTTGGTTCACGAGAATCTAAACGTCACTGCAGAGAGTCGCACAGCCTTTGATCTATGGTATCTTGCGGTCCCAATTGCTTTTGTAAGTAATAACGTGGTCTGTGCCTCTTGGTGAACGACGCGATGCACCTGAGAATTGAAGTAAGAGCATGTATTGACGTACCTCGGGAAGGGATATATGCCGCCTTGATCACAAGGTACGCTAGTAAGGCCGGTAAATCTCTACTCATCCGCGCAACCCCGTGTTGTAGTATTAGTATAGGTTGCTTCGCTCCAGTGGGCAGACGATCTAACCGAGCGGACTCCAACATCAGCAATGGTCATTGGTAGAAATGCCGGTTTTCGTAAAGGGGCATTCACTTAGAGTCCGCCGGATATGACTAATGGACTATTTTTTGAAGGTTTAGCAGCTTTGTGCGGGTTTTGAGCAAGACACGAAAAAATAGGAGCGACTAAAATAAGAAGGGTTGCGGGTGCTAAATCCCTGCGATGAAGCGAGTAGATACTTTAGTTTGATTAGAGCTGACACCTGAGGGGTCTTACACCCATTAGCCCTGTTAGCTAACTCTATAACTTCTGTGCCATGTTGAAATCTGCAGCTCAACGTAGACCTCTACACCCAGGTCCTACACGGTAACTAAAAGGAGCAGACTCCAGCTCCCCTGGTAACCCACTAGTGCAAAGGTCTCCCTTGAAAGGTCACGCTATCGGAGTTTGACTCCTGAGGATACGGACGGCCATGAAGATTCCAGTAGGATGGCGCTGTGGCGGTCCCATATTCTTAGGTCAGATGGAACCTTCCTGATGTGCGCCGTAGTCACAAATGCGCCCATACTTACTGAGGTGCACTGAGCAAGCGAGCCGAGAAGGCGTTTCACGTCAAGTACTGTAGCAACACGCTGATCTGTTAATTTGCTAGGCGTTGTAGTCCTCGGAGGGCCACATACCGGCGCACGACCGGTTGCAAAGATGCAAAATTGGAGCCGATAACATTGAAGTAGAAATCTAAAGACACGTAGGTTCTCGTGCGGTTTTGAGGGTTGGGCGCCGATGTAAGTACGCTCGTGATCGACACGCATCTCGAATCCAAGTACATAAGCTGACATTATATGGTGTCGTCGTATGGGGGTGGGCAATGGCCCAAAGCCGCTGCACTTCTGATGCTAAACCAGTCAAGACTCCGAACCTAGGCAAGAACTCCTAGATCATAACACACAGTTATGATGATCGGTCGGTTATAGCTGTTCCAATAGGCCAGAGAGAAACCGAGTCCACGAATACAAGAACAACCTTGGGTGCCTGTAGGGTCAAACTTTGTCCATCGTACTGAAGCTCAACCGTATTAGGTTTCTTTTCGTCGGACCAGATGAGTGGAACCCTGGCGATCGGTTTACTTGCCATAGCGCCTCCATCGGATAGGTAACCCAAGGCTGAAGGCAACATTAGTATTGCTACAAGCTTGTAGGTGCGATTTCAGACGTCTATGCTCGCGTGAGTCCCGGTCGACTGCATAAGATTTTCTACTCCATCCGAGAAGTTATGACAAAAAGTCGAGCGTAATCAAGATGTATGTGCACGCGACTTTGTGAGACCCGCGGACGACTCCTGGCAAGACCCGAAAATCATTGGAGTGGTGAGGACCCGCCCTGAACATGACTCAACGCACGCTACTAGAATTGTGAACGGAAATCTATAATGTTGGAGACTATAAGGCGCCTGATCTCCAAACACCCGTTCGAGCGTTTTGTGCACGTAGCAACCCCCGAGTCGGGCGGGTCATAAAACGAGTTTTTCGAATGGCATGATGGCGCGGCTTTCTATGGAGGGGTTCGTTTCCGAAAATGCATTAGGAGGAAACAAAATACTCAGCCTCTCGCCACGAGTACATCATTAGGTCCTGAGCGGTATTCTCAATAACTGTGCTCCGTACATTCCGAACGAATATCGGGGATCAACAGACGCGCTACGGTGCTCATGTCATTAAGGCTCGTAAGGACGAGACGAGCTGGATGTGCACAAGCACATTGAACTCTAGCTAGTGGCATCTTCTGTCAAGTGGTTAGCACTATAGCTTTGACAAGCTTTACCTCCTCGCATCTCCACCCTTAGCTTACAGTTCTTCGAAATCGACCAAGCGCCGACTGGATGCGGAAACGTATGCAGCAACAGGCAAATGGGTGTTACCCTGATAGATCATCCCCCAGCGGTCCCCCGCCTTAGACATTGTGGCTGCCAAGATTTACGAATGCAACGCCGGACTGTCGCTCGTCTTTACAGGTGGGAGCTCTTGCATCTGGACCCGATACATTGAATTAGGTTGCCGTGTCCCCGACCGACCACTTTAAAGACGACCGTAACGGTCGTATCTCGAGATAATCCGGTGACCCGCTGGCGGGCGTCTCCCAGCGCGGAAGAGACCAGACTGAGGAGTGGACATAAGGGCTTCAAGTCGGCGTTCTTTCTATCGCGTTACGTGTCCAGCCATACGGGTCAGAAACAAAAAGACATGGGGCCGGAGATTAAGTAGGAATCAGTCACCCTTGGAACCTAACTTATCAGGGGGTCTAGCGAGATAATAGCCTATGGCCTGAGCACTGACTACGTTTGGAGTGGCTGGCATAGTCTCTTGCAGGTTGCTTTTCGTTGATTTCCCGAGAAACAGCATGATAGTTGAGGTTACGGCCGCCCATTCGATTAAAACTCAGCATTTTATCGAAAGCCGCATAATGCGGAGCAACGCGGATAACTGATGTGCATGCAAGATAGGCTGTAGGCTGCTTCAACCCATCGGCAGTGGACACTTAGCGGGAGCTCTAAGAAATATACGTGAGTATAATCCATAATACGCTCGCCGGCACAAGCACGTACCCCGATCCATAGTCTCACGTCCCCTCGGCCGTAAGTGCAGAATTTGTTGACTCGATCCATACGAGTCAAACCTTACGGCGTTAATCTTCAGAACCGGCGTCGTCCACATTCAAATCTAGTTGTGCTAGGACGCACAAAGCCTTATACAGATCTCGAAGTGCCAGTTCAGATGTAGCGAGAACGTATCGACGTGCCAGAGGTCAGTTACGTGAAACACTGCAGGGATTGTGCAAGACCGCGTAGGCACTTACTCGATTCCCCACGATGATCGCGTAGATAGAATTACAACGGGTTTTAACCGTTATAGCGCGTGAGAGTGGGAAAGCACCCTCCCCTGCTAGTATATGTTAGTCACTTCCTTGTACATCGGACTTAGTGATTAGATGTTCGGGACCTCTTCTGATTTGCTCGCTCTCTCGCCAAGATGTGGCTGACGGAGTATGGTACAGAGCGCGCAAGAGGACCGTCCCATGTCCTAAGGAAGCGACTTTGCCCGTTATGGACTGTTCCGGTGAGCCGTCAATGGCCTCGTACAACTTAAAGGGGGTGTGTCTTGTGTAATCCCGCCCTCGGGCAAATGGTTCTGCAATGCAGTCCCTGCGAGGGAGGGCCTTAGGAGGTGCGTTCGCGACATAGAATTCGATTCAGAGTTTTGGGCTACTACCCCGAGTATCATCTGCTGCCGAGATAGGTTAAGCAAGCGCTCTAATCTCGGAGTTTACCGTTTATGTTCAGCCAAACTCACAGCGGTTGCGTCTATACGCAAGTCGGTCAGCTCCACATACTCTATTCCGGCTACGGGTGCGGTGGGTTGTATCCGATTCCGTAGCGCGTTATGCAGTCTCACTGAACGGATGGCAGAATACGTTAGACTAGGGGTCCTTTACGACAGCGCTCCCCGTCTGTAACAATTGCTGGTATTTAAAAGACTGAGTACACATTCACAGGGGTCGAGGTGACGCTCGATAGTAATCTTGCAGTGTACTGTGAACGTAGCAATGCCCCTATCGCTGCTTGTGTGGTAAACAAATCACATAGAAGTACTGCTCCAGAGGGGGACCTCCTCGCTTCTCCTGGCGCCCACAATCCTGAAATGCTTCTTTGAGCCAATTGCCGATCCTAGTCTGTTCAAGGGCGAACCAGGCTTAACTGTATGTTAGTCCTGCCTGTCAGCGGTAGGTAAGAGTGCAACCGATTCTCAGTCATATGCCCTTGCCTGAGCCATACATCGTGGGGGAGTTCGGTCTGAATGTCTGTCCGGTATTGGTATGTCAAGGTTGCACCAACGCCTCAGACCTCACGAGATCGGCCAACCCTAAACCCAAGCGCGTCTCAGCCAGGTGTCGAATCAACAACACAGAAGTGATAAAAAAATACAGAGTTCACATAAAGCGCCTTCTTCGCGCTGCCGATGCAAGTAACCGTAGGATCGCGGTGGGTTCGTTAATTTGACGAGCTACCCGCAAACGACGAGACTACGTCGTGTCGGTTTCGCGTTTACCTAATCGCTATCCCCAAGGATGACTGGCGCACGTCGGTTTGCGCGGCTAAGGTATAATGCATAGTATAAGTCTTACAACGCCCACGACTTCACGAAGAGATACGTGGTGAGCTTCACTTAAGGCCTTATAGGGCCGCTCCTGTGGCCCCCTCAGTCGAAGGCCTCTCCTCTTCACATGCTAGATGCAACTCTAATCATCTTTATGCCCCATACGATTGAGTCGTGACTCTGAGATCGGCGTAGCCGGCACTAATAAATGAAGTTAAGGCCGTTGGTGTCCATGGATTTCGGGACGTCCTAGTCGAAATAAGTCAAGGATTTTGTGTTATGGTGCCCGCTGAGCCACGGATATGACGTCCTCTGAGTTAGTAGCTAAAGTTGTGAACTATGGGTGACTTAGTTTGGGGTTACTGGCCCAAAGGCGGCTTCTGACAGAACCCCGAGAGCGCAGCTTTTGCGAAGGTCACACGCGGTTGAGTACACGTTACTTCAAAGCGCGGGTGGATTTATAAGAGTTGGGGTCTATACGCGGGCACTACGGTTAGCTTACCGTCTTTAGTGAGCGTATCACCTACCGTCCAGGTAGAACCTCATTCTGGACACAGTCAGGACTGAGGTTAGCGGTTATTAAAGGGTAGCTCGCCGCCTGTTTTCACCACGTATGCGACAAGACTGCCACGATATGACGAGAGCAAGTTACTATGTAAACATCACCTCTTTACACGAAGGGCCAGAACAGGAGAATCAGGTACGATAGTAAAAGTACCCGTGAAAATCGGGATACCACCTCGCAACCCCGCAGAGAGAAGGAGGCCAGCATGATTTTTGCGCTCCTCTACTGTGTGGAGAAGCTGCAACATGAAATGTTTCAGCTGTTTGTGTTTACTTCACGTTTTTAAGTGGGTTAGACGGGCGTTCACGTTGCGAACCTGGATTCGCCCGCCGGGCGGACTGTTGCAATGCGAGATTTTCCGACACCCAAATCCAAATAGCTAAGATTGCGAGGGTCTAATAAGGGTATCAGCGGGCCGACGACGCGGTCACACCTCATGTTAACGACGATGTCGTGACACACTCTGGAGTCATGTCCTACCCATGGATGTACAGGTTTTAAGTACATGAGCTCACCTGGCAGAGCCATCTTCTTCACTGCCCGTTTCACAGTACTGAGTGATAACAAGTGGCCATGATACCAAAGGTTAAGGGGGGCAGGAAATACCACGATAGTTCCGGACGAAGCGGGGTTCTACACGTGCCCAATCCCGTGCTTAAATCCGCGCAAGAACAGTACACGTCCTCTACTAGGCCTGTGCCTTAAAGGTCAGTGGATATTTGATGGTCACAGATAATCTCTATGAACGGCATCGACATTATCCTTTCCATCTATTAGGGTTGTGTGACCGAGACTGTTTACTTGGAGGGAATTCATTCTAGGACGTCCTTCTAGCCTTACTCTGTTTCGGCTCGGACTAGCTCAGGTCTTGGACTAGACCTTAGTGGGTTAAATTTCAAGTGCGGCTTATAGTGAGCTAGTCGAGTTACTCCTCCGATGGGCTAGTCTTTCACCGTCTTCCGGTAGAGGGAGCCGCATTCTCGAGATTATAGTCGTGAGATGGGCTCACTGTCCTGTGGAGAATAACCTCCGTGGAGAGTAGTTAACTATACCAGATACAGAGTTGATTTTGCTAAAGGATGGTAATATTTTGCTCTTAACGTTAAGGGTAACATCCACTGTCGGTCATACCTGAAGACCGGTATGATCCGATTTGTAAAGGGTTACTTCGCCTATTGTCCTGCCACCGCGACTCTTGATGCCAGAAGCCAATCGTTTTATTCTTTTCCCCCCGCTTACACGGTCAGGCCGAACTTGCTGGGCTCGTCATCTGGAGACTACTATTTTCTTACCGCACCGCGGGGTCCTACAGTAGACGAGTTGTGCATCGCCAACACTTGTAAATTAGGCGTAATGGCTGCAGCACGCCAATAGGGATTCTCAATTTACGGGGGTCCTGACAGGACGGTCCGGACACTCCTGGAACGTGCTGGAAGGGCACCTTAAGGGGCTGTGAATGTGAGGTCCGATACTCAAGACTTCCTGACTGCCCCTGATTTCGACGGAAGCCTTTTACTATTCATTACCGCCAACAGTCAGGGATGCTCCAAATACATAGCGAAGCGACAGCCTGCTGGTGCGCCGCGCCATGATGTTGGTCTTGCGAGCAGTAAATCCGTCTGCGTGATACGCTATACGGGAACGCTCATGCGCTCGCATCGACGGAGCTAGGCTCGTGATGCTCATCATCATCCTGGAAGGACGGCGTTGGATTTAGTAGGTGGCGTGACTCTCTTAGATTACGTCGGGAAGTCGTGTGAAAAGGTTCCAGCCAAGCGCAAAACGGGTGCCCATGCTATAGGAGCTCCCTGCCCTGGTTCGTGAACCTGGAGAGAGACCTTAGCAATTAAGTTCTGACCTTGCATAAATCCGTAACTATGGCCTGTTCGTCAGTGAGATATAACATTCAAGTATTCGGGTCTGTGGACAGCTTCACTCGGCTGGCAAGTAGCATCCGGGTGACATTGAGCCTTGTATCTTGGGAGTAGCTGAGAAATTTTGATGCGGCTGTCACGTCGTCCGAGCGTGTGTGTATGGGCTAGAGTCTACTAAAAGATGGGCGTGTATAACGGAAATCTGGCGGGCGCGTAGTCGAGAAACTAACATGAAGGTGCTACACACTTTAGGGTACCACGGGAGCATCCATCCACTCCGGACACTATGCAAGCTACGGCTGGCCTGACTAATATTCGTACGTTACGGCCCTTCTTCCTTAACCTGGGGTACGTTGGCGTTGCGTACCCACGCGACAGAAATTGCATATATCAGCAGGGACACGTACATGATACGTTAATAGTCTTTAAGGCCACCGCCAATATATGGGCCGCTAGCGACGTAAACGGCGCATTTCGATGGCGACGGATGCTCGCGCTTTCGCTACACCCCGGCCCCCAGCTAAGCCTCACGACTATGTGACCGCTTCCCGAGGCCCTTCTAAGGTCGGGCCCCTGTTAGGACGGGGGACAGCACACATCTGTAAGTAAAGCCTAAGGTCTAGATCCTACCTTTCTAATGACGTTTCCTCGGTTCTAGCGTACTTAACGTAGTACAATGACAGGGCATCGCGTATCGAAACTCGCGACTTCCAGAGATTCTAGATCGCGTATCGCTAAGAACCCCTGGGTCCAATCACTGGTAGGCAATAATTCCGACAAGATGGTCGCTTCTCCAGCCGGGTACCTTATACGTTAGGTTACTTGGGTGGCAGCTACGAACGCCCTTTAGGCCCGGCCTATTTCATCCTCTAACCCAGGCATATGTTTGGTTTGTATTTTTAGCAGAACGTAAACCCAATCATAAAGCTATAGTGTAAATCCAAGAGCAGCCATCGCCGCCGATCCTTCGAGGTAGATATATATGCCCATTGCCAATTAGCATATCATTGACACGGCCAAACCCCCGGACTTCTGCCTGCATACATACTCGACTTACAAGATAGCCGAAGGGCCTACGTTGACCACCTACGTCTGAAACAATAGAATTGCCAATTGTAGTATACTAGAGTGCGCACGAACGTTTCAGGAATAACTAGTTGTCGTCTCTCGGGGACCTTAAAGAAGGACAGCGTTTAGAGGATACCCACATACAACGGTCACATTGTTTCGTAGGTGAGGATATCTTCGTTTAGGTAGTCGAAATCGCACACATGTTGTTAACAGCACGCGCCTTAATGACAGACGCGCAACACTGCTGCACAGACACCCTTCCACTGGCTCTTTTCGCCAACTGGGACACCGGGCGCAATCGAAGTTCACCATGAACTTGGGCGCGAATCCGCTCGTGACCCGTGCCAGTAAAGGCTTAATGGTCTGGGCAAAGCAAAAGATTGGTCATGGCCAATGTTGTTTCGCCCCACGTACAGTCTGACTGTGACCCTAACGTTCTAAGGTGAAGCTCATGCTCGCGAGCCTTGAACCGGGTCGACGAAGGCTCTACGAAAAACGGACAGACCCACAGAAATTTAAACGCGAGTGAAATTAGGGCTTTTGTGCTGGCTGTGGATAAAAAGGTCGGGTCGATGAGGGTGCGTACACCCATAAAGTGATCGCTGTGAGCGATAGGCCTAAAAGGTGTATAGCGCGACGACAGACTCTATGAAGAATAGTCTTTAAACCCGGCAAGATCAGGTTGGTACCCCTCCAACGTAGGGGACATATTTGAGTCCTTCTTTGGCCGTTGACCCTAGAATAGAGTTTAACAAGTAGTACGAAACACGTATAATATTTACAGAAGTCGACGCACAGCTCCCGGAAGCCCCCACCAGCTAGAGTACGTACGAGTCATTCTGTGCGCACGTTACTCGTTTCCTACGCAAATAGGGTCTGGTGAAAGCTAGTCTTGGGGGGTTTCTGGCAGACTTGGAAGAAGGTACTAACCGCAAACGCGCTACGCTTCCATCGGTCATAACAACATACAAATGTTCTTCGCAACAAAGCCCTCTCCGTCCATAACATCACCATGGACGTCTCCACTTCCCTAGCATTACAATGCGCATAGTGGAATTATGC";
	
	public void testReverseExpectiation() {
		Alphabet alphabet = Alphabet.getDnaAlphabet();
		FiniteMemoryTextModel forwardModel = new MarkovianTextModel(1, alphabet, background);
		FiniteMemoryTextModel reverseModel = forwardModel.reverseTextModel();
		int[] pattern = alphabet.buildIndexArray("CCGGAGTA");
		int[] reversePattern = alphabet.buildIndexArray("ATGAGGCC");
		assertTrue(forwardModel.expectation(pattern) != reverseModel.expectation(pattern));
		// TODO: Think about this stuff: if the background from which models are estimated is shorter, the 
		//       difference between forward and reverse gets larger
		assertEquals(forwardModel.expectation(pattern), reverseModel.expectation(reversePattern),1e-8);
	}

}
